coronavirus
technical: 5 explorative: 5 work status: 5
Life Forms
Major rework in progress, early June 2021
major updates in progress, April 2021]
Summary
A life-forms is a thing with memorized environment interactions and is able to produce rough copies of itself, called progeny. The interactions are stored in a genome. All genomes are made from ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). RNA is common to all life forms on earth. RNA has different function in life: RNA stores and transfers information, RNA can act as enzyme and RNA provide structure. DNA on the other hand is nearly exclusively used for storing information. Life-forms differ in the way they interact with the environment and with each other. Some are more self contained and some less. The interactions determine to a large part how life forms are built and shield their metabolism and vice versa.
Introduction to Life
Defining Life
Life Form
A life form in a given environment is an identifiable thing which is able to initiate re-production of itself giving rise to things which are near the same. These are called progeny or next generation.
In other words, a form of live has memorized environment interactions and passes rough copies of those memories to the next generation.
There are different definitions of life in literature. Some definitions have focus more on the structure than on the functions e.g. sometimes a life form is defined as a cell (what a cell is needs to be defined then) - by such a definition a virus is then considered as a life-form.
Building Blocks of Life Forms
To have specific environment interactions, life forms rely on the property that chemical reactions behave different in different contexts. A context can be radiation, temperature and/or other substances present. A substance enabling or enhancing a certain chemical reaction is called a catalyst:
Catalyst
A substance which increases the rate of a chemical reaction without being permanently changed itself.
Catalysts in the context of lifeforms are called enzymes:
Enzyme
An enzyme is a catalyst in produced by a life form.
The enzymes catalyze specific chemical reactions giving rise to molecules and structures occurring only in the context of life forms. Most enzymes made of RNA or proteins.
All life forms on earth use RNA.
RNA
RNA (= RiboNucleic Acid) are chains of nucleotides.
- … -> nucleotide -> nucleotide -> nucleotide -> nucleotide -> …
The nucleotides are made from three elementary molecules.
Nucleotide
A nucleotide is a triplet of a ribose, phosphate and a purine or pyrimidine base. The ribose is both bound to the phosphate and the base.
So the backbone of RNA is:
- … -> phosphate -> ribose -> phosphate -> ribose -> …
and to each ribose a base is attached. The subunit of the base bound to the ribose has a separate name and is called nucleoside:
Nucleoside
Nucleoside is a purine or pyrimidine base linked to a ribose sugar.
The bases attached determine how two RNA strands bind with each other. The preferred binding patterns of RNA strands is to a RNA strands with matching nucleotides. The binding properties are relevant for:
- The matching RNA pieces which a RNA binds to:
- matching RNA can be of the same RNA strand which results e.g. in circles. This binding patterns determine the 3-d structure of the RNA
- the matching RNA pieces belong to another RNA strand. Which is used for:
- RNA silencing
- RNA duplication
- building of proteins by tRNAs in ribosomes.
- The structure combined with the binding properties determines which reactions and RNA enzyme catalyzes.
The simplest life forms on todays earth are viroids.
Viroid
Viroids are pieces of RNA able to replicate.
All other known life forms on todays earth also encode enzymes made of proteins.
Polypeptides
A polypeptide consists of amino acids chained together.
One or more polypeptides are structured to form a functional unit, called protein:
Protein
A Protein consists of one or more polypeptides.
Polypeptides are produced by ribosomes:
Ribosome
Ribosomes read RNA in positive sense and select a amino acid for each triple of RNA acids and chain these amino acids together to polypeptides.
Translation
Translations is the process when from an RNA sequence a amino acid sequence is constructed.
As noted RNA is able to have nearly all functions related to live e.g. as enzyme. So ribosomes want only to translate very specific RNA and not any RNA molecule lying around. There are special sequences which are recognized by ribosomes to initiate translation.
Translatable RNA
Translatable RNA denotes RNA which is marked to be translated and thus is read by ribosomes.
Translatable RNA is ribosome and life form specific.
The storage piece encoding RNA making up a functional protein or a functional RNA is called a gene:
Gene
A gene denotes a piece of storage encoding a functional polypeptide or RNA strand.
Messenger RNA
Messenger RNA (mRNA) is a special from of translatable RNA which is transcribed from DNA in the cell nucleus and sent to the cytoplasm for translation.
How mRNA is processed is strictly regulated [to check, to confirm and to cite]:
- mRNA be subject to variety of post-transcriptional modifications
- a variety of “helper RNAs” guide the translation to proteins:
- How much protein is produced
- At which ribosomes the proteins are proteins e.g. at the rough endoplasmic reticulum or at free ribosomes in the cytoplasm.
- Possibly helper RNAs are also involved in post-translational modifications [to check]
Memorizing Interactions
Storage Options
Life forms memorize their machinery and structure, which in turn determine the environment interactions. Four kinds of lifetime storage are known to be used on todays earth.
-
ssRNA
single stranded RNA:
- unstable
- difficult to reliably duplicate, recombination possible
-
dsRNA
double stranded RNA:
- somewhat unstable
- somewhat reliable duplication possible
-
ssDNA
single stranded DNA:
- difficult to reliable duplicate, recombination possible
- mediocre stability
-
dsDNA
double stranded DNA:
- very stable
- reliable duplication possible
Systematics
in raw work, April 21 updates in work June 21
To group life forms different criteria can be used:
- Storage Similarity
- storage organization
- stored information = denoted as genetic similarity.
The genetic similarity can be local only due to horizontal gene transfer.
As of 2021 storage information similarity is often used as standard to classify life forms by phylogenetic trees.
- Structural Similarity
Since many structures just developed exactly once during evolution the structural similarity is largely determined by the genetic similarity.
Horizontal gene transfer can induce local structural similarity.
- At the level of molecules: e.g. which enzymes are used
- At the level of smallest units: e.g. enveloped and non-enveloped viruses; having a cell membrane; having a cell nucleus
- At the level of entire organisms or entities.
Systematics of life forms started by this criterion.
- Interactions with other life forms
- autotroph or heterotroph
- able to produce all enzymes or not (viruses)
Grouping Life Forms by Storage System
Life forms can be classified by the storage system they use. All life forms on earth use single stranded RNA at least as temporary storage for translation to proteins, since ribosomes only read single stranded RNA. For permanent storage four storage options are in use. In addition life forms use different access and duplication mechanisms.
Classifying life forms by storage system is known as Baltimore classification of viruses since all life form other than viruses on todays earth use double stranded DNA.
1 Form using RNA only
- uRNA = untranslated RNA
- single RNA strand which catalyzes its duplication
- only occurs in Viroids [to check].
7 Forms using Proteins
7 forms of combinations of lifetime storage and duplication/decode mechanisms are known to be in use on earth, known as Baltimore classification:
- (+)ssRNA = Single stranded RNA, + sense
- genome can be directly read by ribosomes
- replication is done via a (-) RNA strand which is duplicated to many (+) strands
- (-)ssRNA = Single stranded RNA, - sense
- genome needs to be transcribed to (+) stranded RNA before translation in the ribosomes
- replication is done via (+) stranded RNA
- ssDNA = Single-strand DNA
- dsDNA-RT = gapped DNA
- dsRNA = Double strand RNA
- ssRNA-RT = DNA-RNA reverse transcribing
- dsDNA = Double stranded DNA (all cellular life forms)
Notes on Storage
- only dsDNA forms are able to encode all enzymes for their entire metabolism and are able do photosynthesis on todays earth. All other life forms are dependent on some enzymes produced by dsDNA forms and are called viruses.
- Some forms of life alternate the storage formats through their life cycle: ssRNA-RT (retroviruses).
- A more fine grained classification is possible: E.g.
- double stranded DNA forms in turn can be group how the DNA is organized (e.g. bacteria have plasmids).
- Negative stranded RNA viruses often are segmented.
Grouping Life Forms by Structure
Cell Forming Life Forms
in work
As noted all forms of life which encode their entire metabolism are dsDNA based. Many [all ?] of these forms have their metabolism inside semipermeable membranes [all double layer lipid?]. Such a structure is called a cell. Some cells have just the outer membrane:
Prokaryotes
Life forms having an outer membrane but no inner membrane shielding the genome away from the main metabolism. These forms are called prokaryotes (from Greek: pro=before, karyo=kernel).
Some cells are subdivided again by membranes into different compartments which are called cell organelles. If the genome is shielded by a kernel, this organelle is called nucleus.
Eukaryotes
Cell forming life forms shielding with their genome within a nucleus are called eukaryotes (naming done in the 60’s eukaryote = with-a-well-formed-kernel; eu=well and karyo=kernel).
- Prokaryotes
- Eubacteria
- Cyanobacteria
- Bacteria
- Archaea
- Eubacteria
- Eukaryotes
- Plants, Animals and Fungi all belong to the eukaryotes. These eukaryotes form multicellular organisms.
- There are many more eukaryotes, many of them not forming multicellular organisms and thus living as single cells. Even though very divers, these are called protozoa.
Grouping by Interactions
-
Viruses
Viruses are life-forms which either don’t encode or can’t produce all the proteins required for their metabolism. Discussed on the viruses page.
Behavior of Life Forms
in work and incomplete
Explorative Chapter
How Life Forms Respond and Behave depending on Situations
Mechanism for Situation Specific Behavior
Organisms behave different in different environmental situations. The different behaviors can be driven by:
- Lifetime acquired knowledge.
- Inherited behavior and responses, stored in the genome.
- Extern stimulus induced a certain behavior which the life form itself cannot/does not control. E.g. certain physical or chemical stimulus.
Storage form of behavior and responses:
- Stored in neural nets. This is usually the case for lifetime acquired behavior in animals.
- Genetically stored behavior i.e. hard coded in the genome.
Responses to Stimuli
section is unfinished, clarifications are needed and changes likely
Taxis
Taxis denotes directed movement in response to a stimulus.
Kinesis
Kinesis denotes undirected movement in response to a stimulus.
How Life Forms Growth
Plants adapt the environment by different growing patterns.
Tropisms
// The word tropism comes from Greek ‘tropos’ which means turning. In botany tropism is used to describe when plants turn to growth in a specific direction upon a stimulus. Phototropism is when plants growth towards the sunlight and hydrotropism is when the root growth towards water. [wikipedia article on tropism]
Tropism
Tropism denotes here how organisms growth subject to environmental influences. When a life form growths preferable in some settings, the life life form has a tropism for that setting.
Generalized from the usages in virology and botany, given as examples.
Tropism in Botany
In botany, tropism is used how plants growth subject to stimuli.
- When a plant growths towards light this is called phototropism.
- When roots of a plants growth towards water it is hydrotropism.
Tropism in Virology
In virology, tropism is used to describe locations where viruses replicate well. Though the term is not precisely defined and so the usages vary. Mostly the term tropism is used as follows:
- Cell tropism is used to describe cell which support viral replication.
- Tissue tropism denotes the tissues which support viral replication. Tissue tropism is usually determined by diagnostic methods such as the detection of cell damage or virus building blocks (e.g. by PCR).
On this page, a virus has a tropism for a object if the virus is frequently found in the object and has a noticeable effect on that object. Defined in the tropism section in the virus chapter.
- Coronaviruses replicate well in the respiratory tract, thus coronaviruses have a tropism for the respiratory tract.
- SARS-CoV-2 infects ciliated polarized epithelia, thus SARS-CoV-2 has a tropism for these cells.
Ecology
Interactions between Life Forms
Nearly all forms of life are dependent on other forms of life in one way or another. Mostly they need substances for their metabolism which are only produced by other forms of life:
- All forms of life except those who are able to do photosynthesis or use other inorganic energy sources (thermal, chemical) are dependent on organic energy sources i.e. forms of energy produced by other forms of life.
- Besides energy, mammals - including us humans - also need extern sources for vitamins, essential amino acids, essential fatty acids, …
Cell forming forms usually just need the ingredients (raw materials) and are able to produce the enzymes (machines). Where as viruses by definition don’t produce all needed enzymes (machines).
Often life forms specialize, organize and work together to form a more capable entity and thus the overall fitness is increased. Examples of cooperations are symbiosis and organisms.
- Symbiosis
- Conglomerations
- Each member keeps some independence => Entity
- Originating from one unit => Organisms
Symbioses
Many interactions between life forms turned out to be beneficial and reoccur frequently, some of these even evolved into permanent couplings.
Symbiosis
Tight interaction of two different life forms.
Each form providing what it is best at providing at.
The coupling strengths vary:
- Sometimes the couplings are so strong that the coupling is permanent and the combination is a new form of life: E.g. mitochondria as cell organelles.
- Sometime the units keep the ability for separation and can go separate paths again.
Entities
Entity
An entity is a conglomeration of life forms cooperating selflessly to increase the overall fitness.
Notes
- Not all members may have good changes to produce progeny.
- Members often communicate.
Examples
- Bacteria Entities
- Virus Entities
- An organism is a special form of an entity, arising from a single cell by cloning.
Organisms
Many forms of life in the realm of eukaryotes on todays earth e.g. plants, fungi and animals, consists of different looking cells all clones from the same starting cell.
Organism
Start out as a single cell with replicates. At some point the replicates differentiate into specialized cells having different appearances and tasks.
For many questions, organisms are considered as a whole and not the single cells. E.g. we usually are more interested in how fast an organism moves forward/runs and not how fast some single muscle cell contracts.
Mechanism to Control Interactions
Most life forms have have some mechanisms to keep their metabolism balance and control their environment interactions. One part of the balance system is the immune system.
A simple and effective way to control environment interactions, is shielding the metabolism by membranes. The membranes evolved vary in permeability, thickness and rigidity.
Locations of Living
Habitats
Habitat
The places of living of an organism.